Add a sieved, slimmed version of the bax file that was used to produce cmp_mapping.cmp.h5, bam_mapping.bam

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 143367]
WIP on tests

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 143369]
Move alignment IO classes to subdir

They are still accessible as pbcore.io.CmpH5Reader, etc.

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 143370]
Import BAM support, bump to 0.9.2

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 143371]
Make non-executable

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 143372]
Turn on tests for basic BAM functionality

(2 failing tests presently)

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 143373]
Cleaner impl of readLength.  Remove confusingly named alignedLength.

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 143374]
Stronger tests and asserts for clipping

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 143375]
Reenable clipping assert in BAM

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 143376]
Documentation cleanup

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 143377]
Change tests, since clipping behavior is reverted back for the moment

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 143378]
Factor common functionality out into mixin classes

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 143379]
Fix rStart, rEnd logic in clipping

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 143380]
Add some more extensive tests of clipping

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 143381]
import BamAlignment class

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 143382]
Shorten alignment/ to align/

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 143383]
Rename PacBioBamReader to IndexedBamReader

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 143384]
Basic tests for indexed files

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 143385]
Chemistry tests

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 143386]
Remove old cmp.h5 tests

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 143387]